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<p>Alignment represents a set of aligned macromolecule sequences and/or structures.  
 <a href="classmoltk_1_1Alignment__.html#details">More...</a></p>

<p><code>#include &lt;<a class="el" href="Alignment_8hpp_source.html">Alignment.hpp</a>&gt;</code></p>
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Collaboration diagram for moltk::Alignment_&lt; SCORE_TYPE &gt;:</div>
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<p><a href="classmoltk_1_1Alignment__-members.html">List of all members.</a></p>
<table class="memberdecls">
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Classes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">class &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment___1_1Row.html">Row</a></td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Meta-data for one sequence in an <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>.  <a href="classmoltk_1_1Alignment___1_1Row.html#details">More...</a><br/></td></tr>
<tr><td colspan="2"><h2><a name="pub-types"></a>
Public Types</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">enum &#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8">List</a> { <a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8">LIST_SEQUENCE</a>, 
<a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686">LIST_STRUCTURE</a>
 }</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Whether a particular <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> member is a sequence or structure.  <a href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8">More...</a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">typedef <a class="el" href="classmoltk_1_1EString.html">moltk::EString</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a></td></tr>
<tr><td colspan="2"><h2><a name="pub-methods"></a>
Public Member Functions</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#af92538fd947d2503ecd35984642b875c">Alignment_</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Default constructor creates an empty <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>.  <a href="#af92538fd947d2503ecd35984642b875c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a3aebdf39421b1cd2b446a7f23e2209c8">Alignment_</a> (const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;sequence)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment with exactly one sequence.  <a href="#a3aebdf39421b1cd2b446a7f23e2209c8"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#adc92236397e52158d76469813909b6f1">Alignment_</a> (const std::string &amp;alignment_string)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment from fasta sequences or a single sequence string.  <a href="#adc92236397e52158d76469813909b6f1"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a76eab18197656efd9ef9c5c3c1b68307">Alignment_</a> (const char *alignment_string)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create an alignment from fasta sequences or a single sequence string.  <a href="#a76eab18197656efd9ef9c5c3c1b68307"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a96e7fab5bcacdb8c9f1fa2b272cd3dc2">~Alignment_</a> ()</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Delete alignment (destructor)  <a href="#a96e7fab5bcacdb8c9f1fa2b272cd3dc2"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a6aa429375949cd6c7fd4b58960afcc7b">append_sequence</a> (const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;sequence)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Add one sequence to the alignment. Internally, gaps will be removed and encoded into an <a class="el" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>.  <a href="#a6aa429375949cd6c7fd4b58960afcc7b"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a685b48576e005de9013fea1c1457814c">load_string</a> (const std::string &amp;alignment_string)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Add sequences from fasta sequences or a single sequence string.  <a href="#a685b48576e005de9013fea1c1457814c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#abfd24b91e6307001f8268a8b95a78fb1">load_fasta</a> (std::istream &amp;input_stream)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Load fasta format sequences from a C++ stream.  <a href="#abfd24b91e6307001f8268a8b95a78fb1"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a1f9c611fce627e732ba98b4c6bbe7418">load_fasta</a> (const std::string &amp;file_name)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Load fasta sequences from named file.  <a href="#a1f9c611fce627e732ba98b4c6bbe7418"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a530d9e4e4b1c3d1334d6db811a299f10">write_pretty</a> (std::ostream &amp;output_stream) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write a pretty formatted alignment to a C++ stream.  <a href="#a530d9e4e4b1c3d1334d6db811a299f10"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ae154886908be0688f8a3396cce3f618b">write_pretty</a> (const std::string &amp;file_name) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write a pretty formatted alignment to a file.  <a href="#ae154886908be0688f8a3396cce3f618b"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ada1e80499e1d31106f1b319f233b3c60">pretty</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a string containing a pretty formatted alignment.  <a href="#ada1e80499e1d31106f1b319f233b3c60"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ae92aea8bd71e9af1918cebda993da208">write_fasta</a> (std::ostream &amp;output_stream) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format to a C++ stream.  <a href="#ae92aea8bd71e9af1918cebda993da208"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a5b1d1fd583e2843f594dda8f8e85f3c3">write_fasta</a> (const std::string &amp;file_name) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format to a file.  <a href="#a5b1d1fd583e2843f594dda8f8e85f3c3"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a64ffedc0eba04a1a80c349a757275b35">fasta</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a string with <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format.  <a href="#a64ffedc0eba04a1a80c349a757275b35"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a3e3b0dbdb6593e6446ea92a21f5af53c">write_id_table</a> (std::ostream &amp;output_stream) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write table of pairwise sequence identities to a C++ stream.  <a href="#a3e3b0dbdb6593e6446ea92a21f5af53c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a0d0e9fb7403c1f7962109d4fe3e26239">write_id_table</a> (const std::string &amp;file_name) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Write table of pairwise sequence identities to a file.  <a href="#a0d0e9fb7403c1f7962109d4fe3e26239"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a03fb9aaf5c82353cb7152364542654d9">id_table</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Create a string containing table of pairwise sequence identities.  <a href="#a03fb9aaf5c82353cb7152364542654d9"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ac113e59bf55f00ffd7957a39b0d13f5c">get_number_of_columns</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Number of columns (width) of sequence <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>.  <a href="#ac113e59bf55f00ffd7957a39b0d13f5c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">size_t&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6">get_number_of_sequences</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight"><a class="el" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6" title="get_number_of_sequences() includes combined number of both sequences and structures">get_number_of_sequences()</a> includes combined number of both sequences and structures  <a href="#a53d9faa384258178abd19592740deda6"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a1cf784f435f461b69d2cb6fed194e1c8">align</a> (const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;, const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> &amp;, const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> &amp;) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Align two sequence alignments using a pair of precomputed EStrings.  <a href="#a1cf784f435f461b69d2cb6fed194e1c8"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a3320970bfee0ea1058c5a75632fa56b0">get_sequence</a> (size_t index) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Returns the particular sequence or structure at <a class="el" href="classmoltk_1_1Alignment___1_1Row.html" title="Meta-data for one sequence in an Alignment_.">Row</a> index.  <a href="#a3320970bfee0ea1058c5a75632fa56b0"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a3408c640ccc854b0b9af7a593521186a">get_estring</a> (size_t index) const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">The gapping pattern of <a class="el" href="classmoltk_1_1Alignment___1_1Row.html" title="Meta-data for one sequence in an Alignment_.">Row</a> index.  <a href="#a3408c640ccc854b0b9af7a593521186a"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">const SCORE_TYPE &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a14c87e3b0fbf3fc6ddaffb74f18aa539">get_score</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">The precomputed total sum of pairs score of this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>.  <a href="#a14c87e3b0fbf3fc6ddaffb74f18aa539"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a42cec9b9709afe53383953f3f687d16c">set_score</a> (const SCORE_TYPE &amp;s)</td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Set the sum of pairs score for this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. Make sure you put the correct answer!  <a href="#a42cec9b9709afe53383953f3f687d16c"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::string&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a825baa50931639decf5b6989801412f2">repr</a> () const </td></tr>
<tr><td class="mdescLeft">&#160;</td><td class="mdescRight">Low level python string representation of this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>.  <a href="#a825baa50931639decf5b6989801412f2"></a><br/></td></tr>
<tr><td class="memItemLeft" align="right" valign="top"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a0a7ba36b2af5bc886e8bcbc4fbdb4400">set_pretty_width</a> (int width)</td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#aefff61528a8a3210501ee4e517c485b6">get_pretty_width</a> () const </td></tr>
<tr><td colspan="2"><h2><a name="pro-attribs"></a>
Protected Attributes</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">sequences</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html">PDBStructure::Chain</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">structures</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::vector&lt; <a class="el" href="classmoltk_1_1Alignment___1_1Row.html">Row</a> &gt;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">rows</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">SCORE_TYPE&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#ac929115e5fbbfb6a16f537f0d024ff72">m_score</a></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">int&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a></td></tr>
<tr><td colspan="2"><h2><a name="friends"></a>
Friends</h2></td></tr>
<tr><td class="memItemLeft" align="right" valign="top">std::ostream &amp;&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classmoltk_1_1Alignment__.html#a8618745ccb54c7588fa56cfc1f264d3a">operator&lt;&lt;</a> (std::ostream &amp;os, const <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt; &amp;ali)</td></tr>
</table>
<hr/><a name="details" id="details"></a><h2>Detailed Description</h2>
<div class="textblock"><h3>template&lt;class SCORE_TYPE&gt;<br/>
class moltk::Alignment_&lt; SCORE_TYPE &gt;</h3>

<p>Alignment represents a set of aligned macromolecule sequences and/or structures. </p>
</div><hr/><h2>Member Typedef Documentation</h2>
<a class="anchor" id="a67e797edd272010b8e6f7845b825acf4"></a><!-- doxytag: member="moltk::Alignment_::EString" ref="a67e797edd272010b8e6f7845b825acf4" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">typedef <a class="el" href="classmoltk_1_1EString.html">moltk::EString</a> <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

</div>
</div>
<hr/><h2>Member Enumeration Documentation</h2>
<a class="anchor" id="ae82e4fe2134fecfa374499781ec3d2d8"></a><!-- doxytag: member="moltk::Alignment_::List" ref="ae82e4fe2134fecfa374499781ec3d2d8" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
      <table class="memname">
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          <td class="memname">enum <a class="el" href="classmoltk_1_1Alignment__.html#ae82e4fe2134fecfa374499781ec3d2d8">moltk::Alignment_::List</a></td>
        </tr>
      </table>
</div>
<div class="memdoc">

<p>Whether a particular <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> member is a sequence or structure. </p>
<dl><dt><b>Enumerator: </b></dt><dd><table border="0" cellspacing="2" cellpadding="0">
<tr><td valign="top"><em><a class="anchor" id="ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8"></a><!-- doxytag: member="LIST_SEQUENCE" ref="ae82e4fe2134fecfa374499781ec3d2d8a3a38c67cfd20916ed2aca72d487e4eb8" args="" -->LIST_SEQUENCE</em>&nbsp;</td><td>
<p>Item belongs to the sequence list. </p>
</td></tr>
<tr><td valign="top"><em><a class="anchor" id="ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686"></a><!-- doxytag: member="LIST_STRUCTURE" ref="ae82e4fe2134fecfa374499781ec3d2d8aed118ee80047d7db2b9148f435540686" args="" -->LIST_STRUCTURE</em>&nbsp;</td><td>
<p>Item belongs to the structure list. </p>
</td></tr>
</table>
</dd>
</dl>

</div>
</div>
<hr/><h2>Constructor &amp; Destructor Documentation</h2>
<a class="anchor" id="af92538fd947d2503ecd35984642b875c"></a><!-- doxytag: member="moltk::Alignment_::Alignment_" ref="af92538fd947d2503ecd35984642b875c" args="()" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td></td>
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<div class="memdoc">

<p>Default constructor creates an empty <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. </p>

</div>
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<a class="anchor" id="a3aebdf39421b1cd2b446a7f23e2209c8"></a><!-- doxytag: member="moltk::Alignment_::Alignment_" ref="a3aebdf39421b1cd2b446a7f23e2209c8" args="(const Biosequence &amp;sequence)" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td>
          <td class="paramname"><em>sequence</em></td><td>)</td>
          <td></td>
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<div class="memdoc">

<p>Create an alignment with exactly one sequence. </p>

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<a class="anchor" id="adc92236397e52158d76469813909b6f1"></a><!-- doxytag: member="moltk::Alignment_::Alignment_" ref="adc92236397e52158d76469813909b6f1" args="(const std::string &amp;alignment_string)" -->
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> </td>
          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
          <td class="paramname"><em>alignment_string</em></td><td>)</td>
          <td></td>
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<div class="memdoc">

<p>Create an alignment from fasta sequences or a single sequence string. </p>

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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> </td>
          <td>(</td>
          <td class="paramtype">const char *&#160;</td>
          <td class="paramname"><em>alignment_string</em></td><td>)</td>
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<p>Create an alignment from fasta sequences or a single sequence string. </p>

</div>
</div>
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::~<a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a> </td>
          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td><code> [inline]</code></td>
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<p>Delete alignment (destructor) </p>

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</div>
<hr/><h2>Member Function Documentation</h2>
<a class="anchor" id="a1cf784f435f461b69d2cb6fed194e1c8"></a><!-- doxytag: member="moltk::Alignment_::align" ref="a1cf784f435f461b69d2cb6fed194e1c8" args="(const Alignment_ &amp;, const EString &amp;, const EString &amp;) const " -->
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          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&lt; SCORE_TYPE &gt; &amp;&#160;</td>
          <td class="paramname">, </td>
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        <tr>
          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> &amp;&#160;</td>
          <td class="paramname">, </td>
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          <td class="paramkey"></td>
          <td></td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a> &amp;&#160;</td>
          <td class="paramname">&#160;</td>
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          <td></td>
          <td>)</td>
          <td></td><td> const</td>
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<p>Align two sequence alignments using a pair of precomputed EStrings. </p>
<p>This methods is used to create the final <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> after the dynamic programming alignment has completed. </p>

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<a class="anchor" id="a6aa429375949cd6c7fd4b58960afcc7b"></a><!-- doxytag: member="moltk::Alignment_::append_sequence" ref="a6aa429375949cd6c7fd4b58960afcc7b" args="(const Biosequence &amp;sequence)" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&amp; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::append_sequence </td>
          <td>(</td>
          <td class="paramtype">const <a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a> &amp;&#160;</td>
          <td class="paramname"><em>sequence</em></td><td>)</td>
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<p>Add one sequence to the alignment. Internally, gaps will be removed and encoded into an <a class="el" href="classmoltk_1_1EString.html" title="A compact representation of the gapping pattern for one sequence in an alignment.">EString</a>. </p>

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<a class="anchor" id="a64ffedc0eba04a1a80c349a757275b35"></a><!-- doxytag: member="moltk::Alignment_::fasta" ref="a64ffedc0eba04a1a80c349a757275b35" args="() const " -->
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          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>Create a string with <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format. </p>

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          <td class="memname">const <a class="el" href="classmoltk_1_1Alignment__.html#a67e797edd272010b8e6f7845b825acf4">EString</a>&amp; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::get_estring </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>index</em></td><td>)</td>
          <td> const</td>
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<p>The gapping pattern of <a class="el" href="classmoltk_1_1Alignment___1_1Row.html" title="Meta-data for one sequence in an Alignment_.">Row</a> index. </p>

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<a class="anchor" id="ac113e59bf55f00ffd7957a39b0d13f5c"></a><!-- doxytag: member="moltk::Alignment_::get_number_of_columns" ref="ac113e59bf55f00ffd7957a39b0d13f5c" args="() const " -->
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          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>Number of columns (width) of sequence <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. </p>

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          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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<p><a class="el" href="classmoltk_1_1Alignment__.html#a53d9faa384258178abd19592740deda6" title="get_number_of_sequences() includes combined number of both sequences and structures">get_number_of_sequences()</a> includes combined number of both sequences and structures </p>

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          <td>(</td>
          <td class="paramname"></td><td>)</td>
          <td> const<code> [inline]</code></td>
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          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>The precomputed total sum of pairs score of this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. </p>

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          <td class="memname">const <a class="el" href="classmoltk_1_1BaseBiosequence.html">BaseBiosequence</a>&amp; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::get_sequence </td>
          <td>(</td>
          <td class="paramtype">size_t&#160;</td>
          <td class="paramname"><em>index</em></td><td>)</td>
          <td> const</td>
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<p>Returns the particular sequence or structure at <a class="el" href="classmoltk_1_1Alignment___1_1Row.html" title="Meta-data for one sequence in an Alignment_.">Row</a> index. </p>

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          <td class="paramname"></td><td>)</td>
          <td> const</td>
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<p>Create a string containing table of pairwise sequence identities. </p>

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          <td class="memname"><a class="el" href="classmoltk_1_1Alignment__.html">Alignment_</a>&amp; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::load_fasta </td>
          <td>(</td>
          <td class="paramtype">std::istream &amp;&#160;</td>
          <td class="paramname"><em>input_stream</em></td><td>)</td>
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<p>Load fasta format sequences from a C++ stream. </p>

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          <td>(</td>
          <td class="paramtype">const std::string &amp;&#160;</td>
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<p>Load fasta sequences from named file. </p>

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template&lt;class SCORE_TYPE&gt; </div>
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<p>Add sequences from fasta sequences or a single sequence string. </p>

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<p>Create a string containing a pretty formatted alignment. </p>

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<a class="anchor" id="a825baa50931639decf5b6989801412f2"></a><!-- doxytag: member="moltk::Alignment_::repr" ref="a825baa50931639decf5b6989801412f2" args="() const " -->
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<p>Low level python string representation of this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. </p>

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<a class="anchor" id="a0a7ba36b2af5bc886e8bcbc4fbdb4400"></a><!-- doxytag: member="moltk::Alignment_::set_pretty_width" ref="a0a7ba36b2af5bc886e8bcbc4fbdb4400" args="(int width)" -->
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</div>
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<a class="anchor" id="a42cec9b9709afe53383953f3f687d16c"></a><!-- doxytag: member="moltk::Alignment_::set_score" ref="a42cec9b9709afe53383953f3f687d16c" args="(const SCORE_TYPE &amp;s)" -->
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<p>Set the sum of pairs score for this <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a>. Make sure you put the correct answer! </p>

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<a class="anchor" id="ae92aea8bd71e9af1918cebda993da208"></a><!-- doxytag: member="moltk::Alignment_::write_fasta" ref="ae92aea8bd71e9af1918cebda993da208" args="(std::ostream &amp;output_stream) const " -->
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<p>Write <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format to a C++ stream. </p>

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</div>
<a class="anchor" id="a5b1d1fd583e2843f594dda8f8e85f3c3"></a><!-- doxytag: member="moltk::Alignment_::write_fasta" ref="a5b1d1fd583e2843f594dda8f8e85f3c3" args="(const std::string &amp;file_name) const " -->
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template&lt;class SCORE_TYPE&gt; </div>
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<div class="memdoc">

<p>Write <a class="el" href="classmoltk_1_1Alignment__.html" title="Alignment represents a set of aligned macromolecule sequences and/or structures.">Alignment_</a> in fasta format to a file. </p>

</div>
</div>
<a class="anchor" id="a3e3b0dbdb6593e6446ea92a21f5af53c"></a><!-- doxytag: member="moltk::Alignment_::write_id_table" ref="a3e3b0dbdb6593e6446ea92a21f5af53c" args="(std::ostream &amp;output_stream) const " -->
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<p>Write table of pairwise sequence identities to a C++ stream. </p>

</div>
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<a class="anchor" id="a0d0e9fb7403c1f7962109d4fe3e26239"></a><!-- doxytag: member="moltk::Alignment_::write_id_table" ref="a0d0e9fb7403c1f7962109d4fe3e26239" args="(const std::string &amp;file_name) const " -->
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template&lt;class SCORE_TYPE&gt; </div>
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<p>Write table of pairwise sequence identities to a file. </p>

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<a class="anchor" id="a530d9e4e4b1c3d1334d6db811a299f10"></a><!-- doxytag: member="moltk::Alignment_::write_pretty" ref="a530d9e4e4b1c3d1334d6db811a299f10" args="(std::ostream &amp;output_stream) const " -->
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<p>Write a pretty formatted alignment to a C++ stream. </p>

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<a class="anchor" id="ae154886908be0688f8a3396cce3f618b"></a><!-- doxytag: member="moltk::Alignment_::write_pretty" ref="ae154886908be0688f8a3396cce3f618b" args="(const std::string &amp;file_name) const " -->
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<p>Write a pretty formatted alignment to a file. </p>

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<hr/><h2>Friends And Related Function Documentation</h2>
<a class="anchor" id="a8618745ccb54c7588fa56cfc1f264d3a"></a><!-- doxytag: member="moltk::Alignment_::operator&lt;&lt;" ref="a8618745ccb54c7588fa56cfc1f264d3a" args="(std::ostream &amp;os, const moltk::Alignment_&lt; SCORE_TYPE &gt; &amp;ali)" -->
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          <td class="paramkey"></td>
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<hr/><h2>Member Data Documentation</h2>
<a class="anchor" id="ac929115e5fbbfb6a16f537f0d024ff72"></a><!-- doxytag: member="moltk::Alignment_::m_score" ref="ac929115e5fbbfb6a16f537f0d024ff72" args="" -->
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<div class="memdoc">

</div>
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<a class="anchor" id="a7b353afe4712a512a87f5ef9e61af88c"></a><!-- doxytag: member="moltk::Alignment_::pretty_width" ref="a7b353afe4712a512a87f5ef9e61af88c" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">int <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html#a7b353afe4712a512a87f5ef9e61af88c">pretty_width</a><code> [protected]</code></td>
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<div class="memdoc">

</div>
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<a class="anchor" id="a468e2e5c2a46fb3b163805942a533c08"></a><!-- doxytag: member="moltk::Alignment_::rows" ref="a468e2e5c2a46fb3b163805942a533c08" args="" -->
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          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1Alignment___1_1Row.html">Row</a>&gt; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html#a468e2e5c2a46fb3b163805942a533c08">rows</a><code> [protected]</code></td>
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</div>
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<a class="anchor" id="afb22dd1d74614d10f0633ce8bfb2f6a6"></a><!-- doxytag: member="moltk::Alignment_::sequences" ref="afb22dd1d74614d10f0633ce8bfb2f6a6" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1Biosequence.html">Biosequence</a>&gt; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html#afb22dd1d74614d10f0633ce8bfb2f6a6">sequences</a><code> [protected]</code></td>
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<a class="anchor" id="ab7ef21f5246cf6aeeb64e199d02ff8fa"></a><!-- doxytag: member="moltk::Alignment_::structures" ref="ab7ef21f5246cf6aeeb64e199d02ff8fa" args="" -->
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template&lt;class SCORE_TYPE&gt; </div>
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          <td class="memname">std::vector&lt;<a class="el" href="classmoltk_1_1PDBStructure_1_1Chain.html">PDBStructure::Chain</a>&gt; <a class="el" href="classmoltk_1_1Alignment__.html">moltk::Alignment_</a>&lt; SCORE_TYPE &gt;::<a class="el" href="classmoltk_1_1Alignment__.html#ab7ef21f5246cf6aeeb64e199d02ff8fa">structures</a><code> [protected]</code></td>
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</div>
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<hr/>The documentation for this class was generated from the following file:<ul>
<li>moltk/<a class="el" href="Alignment_8hpp_source.html">Alignment.hpp</a></li>
</ul>
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